Interpretive Summary: Manipulating ruminal fermentation has long been attempted to optimize rumen microbial ecosystem output in order to meet unsatisfied needs from the world’s burgeoning human population for meat, dairy and wool and to mitigate the environmental footprint of animal agriculture. Metagenomic analysis was conducted on two rumen samples. Our results revealed as many as 16 bacterial phyla from a single rumen microbial community fed with a hay based diet. Rich diversity was also reflected by a broad phylogenetic representation of organisms in the rumen, from fungi, green algae, protists, to parasitic nematodes. Sodium propionate, one of the key volatile fatty acids for ruminants, seemed to create a more favorable environment for Gram+ bacteria than Gram-. The changes in microbiota composition induced by propionate treatment resulted in a drastic shift in rumen functional profiles. Overall ruminal peptidase abundance was substantially reduced, leading to a higher ruminal nitrogen retention and improved nitrogen utilization efficiency. The vast majority of predicted proteins from rumen metagenomes remain un-annotated, suggesting that substantial unexplored microbial diversity exists in the rumen. Our results provided insight into the rumen microbiota constituents and their interactions. The knowledge obtained is essential in predicting ruminal functions and ruminant nutrition, the first step towards a solid understanding of rumen microbial ecosystem.

Technical Abstract:
Optimizing rumen microbial ecosystem output is essential towards improved ruminant agriculture. Ruminal infusion or intake of propionate, one of the predominant volatile fatty acids, has important implications for host physiology. However, how the rumen microbiota responds to propionate administration has not been documented or quantified. In this study, the functional shifts and phylogenetic distribution of the rumen microbiota in response to sodium propionate were characterized using metagenomic analyses of approximately eight gigabases of short-read sequences generated from two rumen metagenomes. Approximately 1 million proteins predicted from assembled contigs were annotated against the Pfam database. Propionate intake induced a drastic change in the rumen microbiota constituents, including significant changes in 313 Pfam protein families at FDR <10% and P<0.004, and a substantial reduction in peptidases such as the critical DPP-IV. Treatment appeared to reduce the fibrolytic bacterium Fibrobacter succinogenes, possibly via a propionate-coupled feedback loop. Seventy glycoside hydrolase families were identified from the rumen microbiota. Propionate intake seemed to create a more favorable environment for Gram+ bacteria than Gram-. Our results suggested substantial unexplored microbial diversity in the rumen and provided insight into responsiveness of the rumen microbiota and its implications in ruminant physiology and nutrition.